annotate VCF files for poly repeats
meta
:map
Groovy Map containing VCF information
vcf
:file
Groovy Map containing reference genome information for vcf
*.{vcf,bcf,vcf.gz,bcf.gz}
tbi
Alternative VCF file index
*.tbi
regions_file
Regions file
meta2
Groovy Map containing fasta information
fasta
Groovy Map containing reference genome information for fai reference fasta file
*.fasta
meta3
Groovy Map containing fasta.fai information
fai
Groovy Map containing reference genome information for fai
*.fasta.fai
meta4
Groovy Map containing fasta.dict information
dict
Groovy Map containing reference genome information for GATK sequence dictionary
*.dict
Groovy Map containing VCF information e.g. [ id:‘test’, single_end:false ]
*.${extension}
VCF filtered output file
csi
*.csi
Default VCF file index
versions_jvarkit
${task.process}
:string
The name of the process
jvarkit
The name of the tool
jvarkit -v
:eval
The expression to obtain the version of the tool
versions_bcftools
bcftools
bcftools --version |& sed '1!d;s/bcftools //'
versions
Java utilities for Bioinformatics.
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
